Return to study ST002223 main page
MB Sample ID: SA212089
| Local Sample ID: | MS56-023 |
| Subject ID: | SU002309 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU002309 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| MS56-023 | SA212089 | FL025882 | mouse | Species |
| MS56-023 | SA212089 | FL025882 | heart | Organ |
| MS56-023 | SA212089 | FL025882 | tissue | Matrix |
Collection:
| Collection ID: | CO002302 |
| Collection Summary: | Mice were culled by cervical dislocation and tissue samples from hearts, livers, kidneys, and lungs were collected and split into two halves. One half was snap frozen in liquid nitrogen and stored at -80°C until further processing. The second half was used for interstitial fluid extraction using a protocol adapted from Sullivan et al. 2019 (https://doi.org/10.7554/eLife.44235) |
| Sample Type: | Mouse tissues and interstitial fluids |
Treatment:
| Treatment ID: | TR002321 |
| Treatment Summary: | No further treatment was carried out. |
Sample Preparation:
| Sampleprep ID: | SP002315 |
| Sampleprep Summary: | For tissue extraction, samples were homogenized in metabolite extraction buffer using the proportion 25 μl/mg of buffer with Precellys Lysing tubes (Bertin Instruments). After that, extracts were kept in the freezer overnight and the following day centrifuged twice at max speed at 4C˚ to remove the protein precipitates. Equal volumes of supernatants were spiked in with 13C arginine (Cambridge Isotopes) for quantification of arginine content. For extraction of the tissue interstitial for interstitial fluid extraction, the organ was washed in saline solution and then a portion was centrifuged at for 10 min at 4°C at 106 x g using 20 µm nylon filters (Spectrum Labs, Waltham, MA, 148134) affixed on top of 2 ml Eppendorf tubes. 1μl of the eluate was extracted in 45μl of extraction buffer and frozen overnight. The following day, all extracted were centrifuged twice at max speed at 4C˚to remove the protein precipitates. Supernatants were finally spiked in with 13C arginine (Cambridge Isotopes) for arginine quantification. |
Combined analysis:
| Analysis ID | AN003632 |
|---|---|
| Analysis type | MS |
| Chromatography type | HILIC |
| Chromatography system | Thermo Dionex Ultimate 3000 |
| Column | SeQuant ZIC-pHILIC |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Q Exactive Orbitrap |
| Ion Mode | UNSPECIFIED |
| Units | peak area |
Chromatography:
| Chromatography ID: | CH002687 |
| Chromatography Summary: | Chromatographic separation of metabolites was achieved using a Millipore Sequant ZIC-pHILIC analytical column (5 µm, 2.1 × 150 mm) equipped with a 2.1 × 20 mm guard column (both 5 mm particle size) with a binary solvent system. Solvent A was 20 mM ammonium carbonate, 0.05% ammonium hydroxide; Solvent B was acetonitrile. The column oven and autosampler tray were held at 40 °C and 4 °C, respectively. The chromatographic gradient was run at a flow rate of 0.200 mL/min as follows: 0–2 min: 80% B; 2-17 min: linear gradient from 80% B to 20% B; 17-17.1 min: linear gradient from 20% B to 80% B; 17.1-23 min: hold at 80% B. Samples were randomized and the injection volume was 5 µl. A pooled quality control (QC) sample was generated from an equal mixture of all individual samples and analysed interspersed at regular intervals. |
| Instrument Name: | Thermo Dionex Ultimate 3000 |
| Column Name: | SeQuant ZIC-pHILIC |
| Column Temperature: | 40 |
| Flow Gradient: | 0-2 min: 80% B; 2-17 min: linear gradient from 80% B to 20% B; 17-17.1 min: linear gradient from 20% B to 80% B; 17.1-23 min: hold at 80% B |
| Flow Rate: | 0.200 mL/min |
| Solvent A: | 100% water; 20 mM ammonium carbonate; 0.05% ammonium hydroxide |
| Solvent B: | 100% acetonitrile |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS003383 |
| Analysis ID: | AN003632 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Metabolites were measured with a Thermo Scientific Q Exactive Hybrid Quadrupole-Orbitrap Mass spectrometer (HRMS) coupled to a Dionex Ultimate 3000 UHPLC. The mass spectrometer was operated in full-scan, polarity-switching mode, with the spray voltage set to +4.5 kV/-3.5 kV, the heated capillary held at 320 °C, and the auxiliary gas heater held at 280 °C. The sheath gas flow was set to 55 units, the auxiliary gas flow was set to 15 units, and the sweep gas flow was set to 0 unit. HRMS data acquisition was performed in a range of m/z = 70–900, with the resolution set at 70,000, the AGC target at 1 × 106, and the maximum injection time (Max IT) at 120 ms. Metabolite identities were confirmed using two parameters: (1) precursor ion m/z was matched within 5 ppm of theoretical mass predicted by the chemical formula; (2) the retention time of metabolites was within 5% of the retention time of a purified standard run with the same chromatographic method. Chromatogram review and peak area integration were performed using the Thermo Fisher software Tracefinder 5.0 and the peak area for each detected metabolite was normalized against the total ion count (TIC) of that sample to correct any variations introduced from sample handling through instrument analysis. The normalized areas were used as variables for further statistical data analysis. |
| Ion Mode: | UNSPECIFIED |
